ArticleGenome research2007
A systems biology approach for pathway level analysis.
Article in Genome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 741 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
741 citing papers in PubMed.
- High-Intensity interval training reduces transcriptomic age: A randomized controlled trial.Aging cell · 2023Trial
- DLL3 serves as a pivotal hub bridging malignant progression and immunosuppression in NECC with therapeutic implications validated via the organoid-TIL co-culture system.Genes & diseases · 2026Article
- LPS stimulation reveals male and female dimorphism in human iPSC-derived macrophages.iScience · 2026Article
- Mitochondrial oxidative stress in skeletal muscle alters metabolic signaling responses to acute muscle contraction.Free radical biology & medicine · 2026Article
- Lithium chloride in vitro treatment shows potential to rescue the neuronal phenotype caused by WDFY3 haploinsufficiency.Molecular psychiatry · 2026Article
- Proteomics in Ataxia Telangiectasia Fibroblasts Revealed Disease Hallmarks Recovered by ATM Variants.International journal of molecular sciences · 2026Article
- A high-dimensional benchmark of objective functions and biological resolutions for personalized metabolic phenotyping.Briefings in bioinformatics · 2026Article
- AnBiomedicines · 2026Article
- Periostin drives psoriasis progression through the stimulation of cutaneous nerve fibers.iScience · 2026Article
- Proteomic Insights Into Human Induced Regulatory T Cells: The Role of LPXN and CD160 in Immune Suppression.Molecular & cellular proteomics : MCP · 2026Article
- Adaptation of the Transcriptome and miRNAome in Response to Hepatocellular Hypoxia.International journal of molecular sciences · 2026Article
- PGC-1α pathway dysregulation disrupts myofiber specification in a mouse model of SBMA.JCI insight · 2026Article
- Perturbed Inflammatory, Proliferation, Regulatory, And Neurodegeneration Signaling Pathways Are Associated With Trait Anxiety In Cancer Survivors.Research square · 2026Article
- Unsupervised Deep Representation Learning and Probabilistic Clustering for the Systems-Level Discovery of Germline Mutation Signatures in Pediatric Cancers.Biomedicines · 2026Article
- Newly identified invasion drivers define the tumor front in oral squamous cell carcinoma.Cell death discovery · 2026Article
- Single-cell and spatial transcriptomes reveal oligodendrocyte remodeling fatty acid metabolism microenvironment of lung cancer brain metastases.Journal of translational medicine · 2026Article
- The integrated developmental stress response (ISR-DASR) shift reveals a functional transition from cellular to stem cell organismal adaptation.Scientific reports · 2026Article
- SIRT1-NCOR2 Corepressor Modulates Trophoblast-Macrophage Interactions in Preeclampsia.Hypertension (Dallas, Tex. : 1979) · 2026Article
- Selective reduction of KCNA4 in vulnerable glutamatergic-serotonin neurons of the dorsal raphe nucleus in Alzheimer's disease.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2026Article
- Antimicrobial coated intracortical probes reduce invading microbe abundance and subsequent neuroinflammation.Biomaterials · 2026Article
681 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
A common challenge in the analysis of genomics data is trying to understand the underlying phenomenon in the context of all complex interactions taking place on various signaling pathways. A statistical approach using various models is universally used to identify the most relevant pathways in a given experiment. Here, we show that the existing pathway analysis methods fail to take into consideration important biological aspects and may provide incorrect results in certain situations. By using a systems biology approach, we developed an impact analysis that includes the classical statistics but also considers other crucial factors such as the magnitude of each gene's expression change, their type and position in the given pathways, their interactions, etc. The impact analysis is an attempt to a deeper level of statistical analysis, informed by more pathway-specific biology than the existing techniques. On several illustrative data sets, the classical analysis produces both false positives and false negatives, while the impact analysis provides biologically meaningful results. This analysis method has been implemented as a Web-based tool, Pathway-Express, freely available as part of the Onto-Tools (http://vortex.cs.wayne.edu).
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.